samer@0: package samer.mds;
samer@0: 
samer@0: import samer.core.*;
samer@0: import samer.core.types.*;
samer@0: import samer.maths.*;
samer@0: import samer.tools.*;
samer@0: 
samer@0: /**
samer@0:      This is a version that does not use a separete metric and
samer@0: 	stress function: the stress function is defined directly in terms
samer@0: 	of the displacement vectors between objects. The distances
samer@0: 	are now  generalised link targets.
samer@0:  */
samer@0: public class NewMDS extends MDSBase
samer@0: {
samer@0: 	Stress		stress;		// stress function
samer@0: 
samer@0: 	public interface Stress {
samer@0: 		/** accumulate stress due to a link given end points, return gradient
samer@0: 			in g, return true if gradient is usable, false of gradient is bad (eg singularity) */
samer@0: 		boolean add( double target, double [] x, double [] y, double [] g);
samer@0: 
samer@0: 		/** return normalised stress and reset for next time */
samer@0: 		double done();
samer@0: 
samer@0: 		/** return last value returned by done() */
samer@0: 		double get();
samer@0: 	}
samer@0: 
samer@0: 	public static class Laplacian implements Stress {
samer@0: 		double S=0, a=0;
samer@0: 		int			n=0, E;
samer@0: 
samer@0: 		public Laplacian(int E) { this.E=E; }
samer@0: 		
samer@0: 		/** add stress due to link from x to y. Force in link is returned in g.
samer@0: 			Target is assumed to be a length measured according to a 1-norm. 
samer@0: 		*/
samer@0: 		public boolean add( double target, double [] x, double [] y, double [] g) {
samer@0: 			double b=0;
samer@0: 			for (int i=0; i<E; i++) {
samer@0: 				b+=Math.abs(x[i]-y[i]);
samer@0: 				g[i]=sgn(x[i]-y[i]);
samer@0: 			}
samer@0: 			b += sqr(b/target-1); n++;
samer@0: 			Mathx.mul(g,(b-target)/(target*target));
samer@0: 			return true;
samer@0: 		}
samer@0: 		
samer@0: 		/** finish accumulating stress terms: reset accumulators for next
samer@0: 			iteration and return normalised stress (ie per link) 
samer@0: 		*/
samer@0: 		public double done() { S=a/n; a=0; n=0; return S; }
samer@0: 		
samer@0: 		/** return last stress value */
samer@0: 		public double get() { return S; }
samer@0: 		private final static double sqr(double t) {return t*t;}
samer@0: 		private final static double sgn(double t) {
samer@0: 			if (t<0) return -1; else if (t>0) return +1; else return 0;
samer@0: 		}
samer@0: 	}
samer@0: 
samer@0: 	public NewMDS(Matrix p)	{
samer@0: 		super(p);
samer@0: 		Shell.push(node);
samer@0: 		stress=new Laplacian(E);
samer@0: 		Shell.pop();
samer@0: 	}
samer@0: 
samer@0: 	public void run()
samer@0: 	{
samer@0: 		double [][] _P=P.getArray();
samer@0: 		double	d, dS;
samer@0: 		int 		i, j, k;
samer@0: 
samer@0: 		// accumulate all forces on a per object basis
samer@0: 
samer@0: 		for (k=0; k<N; k++) Mathx.zero(F[k]); // zero out object forces
samer@0: 		for (k=0; k<M; k++) {			// for each link
samer@0: 			i=l1[k]; j=l2[k]; 				// object indices
samer@0: 			if (stress.add(D[k],_P[j],_P[i],f)) {
samer@0: 				Mathx.add(E,F[i],f);
samer@0: 				Mathx.sub(E,F[j],f);
samer@0: 			}
samer@0: 		}
samer@0: 		S.set(stress.done());
samer@0: 
samer@0: 		// now move objects at the ends of each link,
samer@0: 		// but only the first E dimensions
samer@0: 		for (k=0; k<N; k++) Mathx.muladd(E,_P[k],F[k],rate.value);
samer@0: 		P.changed();
samer@0: 	}
samer@0: }